Category

Sam/Bam Manipulation


Usage

java -jar picard.jar GenotypeConcordance CALL_VCF=input.vcf CALL_SAMPLE=sample_name O=gc_concordance.vcf TRUTH_VCF=truth_set.vcf TRUTH_SAMPLE=truth_sample#


Manual

TRUTH_VCF (File)    The VCF containing the truth sample Required.
CALL_VCF (File)    The VCF containing the call sample Required.
OUTPUT (File)    Basename for the two metrics files that are to be written. Resulting files will be .genotype_concordance_summary_metrics and .genotype_concordance_detail_metrics. Required.
OUTPUT_VCF (Boolean)    Output a VCF annotated with concordance information. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
TRUTH_SAMPLE (String)    The name of the truth sample within the truth VCF. Not required if only one sample exists. Default value: null.
CALL_SAMPLE (String)    The name of the call sample within the call VCF. Not required if only one sample exists. Default value: null.
INTERVALS (File)    One or more interval list files that will be used to limit the genotype concordance. Note - if intervals are specified, the VCF files must be indexed. Default value: null. This option may be specified 0 or more times.
INTERSECT_INTERVALS (Boolean)    If true, multiple interval lists will be intersected. If false multiple lists will be unioned. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
MIN_GQ (Integer)    Genotypes below this genotype quality will have genotypes classified as LowGq. Default value: 0. This option can be set to 'null' to clear the default value.
MIN_DP (Integer)    Genotypes below this depth will have genotypes classified as LowDp. Default value: 0. This option can be set to 'null' to clear the default value.
OUTPUT_ALL_ROWS (Boolean)    If true, output all rows in detailed statistics even when count == 0. When false only output rows with non-zero counts. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
USE_VCF_INDEX (Boolean)    If true, use the VCF index, else iterate over the entire VCF. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
MISSING_SITES_HOM_REF (Boolean)    Default is false, which follows the GA4GH Scheme. If true, missing sites in the truth set will be treated as HOM_REF sites and sites missing in both the truth and call sets will be true negatives. Useful when hom ref sites are left out of the truth set. This flag can only be used with a high confidence interval list. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}


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